Pierrick Roger
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:09 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2025-03-18 12:58:32 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 13:00:13 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 101.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-18 12:59:24.303][biodb::testContext]
biodb.INFO [2025-03-18 12:59:24.308][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:24.309][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-18 12:59:24.310][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:24.311][biodb::testContext]
biodb.INFO [2025-03-18 12:59:24.319][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:24.322][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:24.332][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:24.333][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-18 12:59:24.335][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-18 12:59:24.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.339][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-18 12:59:24.379][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-18 12:59:24.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.382][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-18 12:59:24.383][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-18 12:59:24.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.387][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-18 12:59:24.388][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-18 12:59:24.390][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-18 12:59:24.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.393][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-18 12:59:24.394][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-18 12:59:24.395][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-18 12:59:24.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.398][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-18 12:59:24.399][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-18 12:59:24.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.402][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-18 12:59:24.403][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-18 12:59:24.404][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-18 12:59:24.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.407][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-18 12:59:24.408][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-18 12:59:24.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.411][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-18 12:59:24.412][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-18 12:59:24.413][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-18 12:59:24.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.416][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:24.417][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-18 12:59:24.418][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-18 12:59:24.419][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-18 12:59:24.420][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-18 12:59:24.421][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-18 12:59:24.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.426][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-18 12:59:24.427][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-18 12:59:24.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.431][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-18 12:59:24.432][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-18 12:59:24.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.436][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-18 12:59:24.437][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-18 12:59:24.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.440][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-18 12:59:24.441][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-18 12:59:24.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.444][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-18 12:59:24.445][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-18 12:59:24.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.448][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:24.449][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-18 12:59:24.466][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-18 12:59:24.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.470][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-18 12:59:24.470][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-18 12:59:24.471][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-18 12:59:24.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.478][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-18 12:59:24.512][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.528][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-18 12:59:24.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:24.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.532][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.532][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.534][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:24.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:24.536][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.536][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-18 12:59:24.537][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:24.538][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.539][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.540][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:24.540][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:24.540][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:24.540][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:24.540][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:24.541][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:24.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.543][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:24.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.553][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:24.555][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:24.556][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.556][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.557][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-18 12:59:24.559][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.560][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:24.561][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.562][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:24.562][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.563][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.564][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.565][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.566][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:24.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:24.567][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.568][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-18 12:59:24.569][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:24.570][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.570][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.571][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:24.571][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:24.571][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:24.571][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:24.571][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:24.572][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:24.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.574][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:24.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.577][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.578][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.578][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:24.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:24.580][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.581][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.582][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-18 12:59:24.583][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.584][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-18 12:59:24.585][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:24.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.588][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.588][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.589][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.590][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:24.591][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:24.592][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.592][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-18 12:59:24.593][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:24.594][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.596][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:24.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:24.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.601][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.602][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:24.604][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:24.605][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.606][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.607][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-18 12:59:24.609][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.610][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:24.611][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.612][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:24.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.616][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:24.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:24.617][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.618][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-18 12:59:24.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:24.620][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.621][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:24.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.624][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:24.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.627][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.627][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.628][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:24.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:24.630][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.631][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:24.635][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:24.636][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.708][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-18 12:59:24.713][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-18 12:59:24.714][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-18 12:59:24.716][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-18 12:59:24.717][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:24.718][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:24.719][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:24.720][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:24.721][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-18 12:59:24.722][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:24.724][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:24.725][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-18 12:59:24.726][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:24.727][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:24.728][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-18 12:59:24.729][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:24.730][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-18 12:59:24.732][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-18 12:59:24.733][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:24.734][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-18 12:59:24.735][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-18 12:59:24.736][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-18 12:59:24.737][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-18 12:59:24.739][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-18 12:59:24.740][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-18 12:59:24.741][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-18 12:59:24.742][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-18 12:59:24.743][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-18 12:59:24.744][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-18 12:59:24.746][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-18 12:59:24.747][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-18 12:59:24.748][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-18 12:59:24.749][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-18 12:59:24.750][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-18 12:59:24.751][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-18 12:59:24.752][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-18 12:59:24.754][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-18 12:59:24.755][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-18 12:59:24.756][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-18 12:59:24.757][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-18 12:59:24.758][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-18 12:59:24.759][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-18 12:59:24.761][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-18 12:59:24.762][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-18 12:59:24.763][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-18 12:59:24.764][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-18 12:59:24.765][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-18 12:59:24.766][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-18 12:59:24.768][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-18 12:59:24.769][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-18 12:59:24.770][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-18 12:59:24.771][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-18 12:59:24.772][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-18 12:59:24.773][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-18 12:59:24.774][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-18 12:59:24.775][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-18 12:59:24.777][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-18 12:59:24.778][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-18 12:59:24.779][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-18 12:59:24.780][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-18 12:59:24.781][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-18 12:59:24.783][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-18 12:59:24.784][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-18 12:59:24.785][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-18 12:59:24.786][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-18 12:59:24.787][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-18 12:59:24.788][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:24.790][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:24.791][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-18 12:59:24.792][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-18 12:59:24.793][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-18 12:59:24.795][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-18 12:59:24.797][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-18 12:59:24.799][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-18 12:59:24.800][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-18 12:59:24.802][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-18 12:59:24.803][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-18 12:59:24.804][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-18 12:59:24.805][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-18 12:59:24.807][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-18 12:59:24.808][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-18 12:59:24.809][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-18 12:59:24.810][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-18 12:59:24.816][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-18 12:59:24.818][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:24.822][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:24.823][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.824][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:24.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:24.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:24.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:24.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:24.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:24.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:24.927][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:24.937][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-18 12:59:24.939][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.940][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.941][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:24.943][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.943][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.944][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.945][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-18 12:59:24.946][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-18 12:59:24.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:24.948][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.948][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-18 12:59:24.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-18 12:59:24.950][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-18 12:59:24.951][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:24.952][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:24.952][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:24.952][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:24.953][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-18 12:59:24.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.955][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:24.956][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:24.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:24.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:24.958][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:24.958][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-18 12:59:24.959][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:24.960][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:24.961][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:24.961][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-18 12:59:24.961][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-18 12:59:24.967][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:24.969][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:24.971][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-18 12:59:24.972][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:24.974][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:24.975][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:25.006][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-18 12:59:25.007][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-18 12:59:25.012][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-18 12:59:25.017][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-18 12:59:25.022][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:25.022][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:25.024][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-18 12:59:25.025][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-18 12:59:25.036][biodb::testThat]
biodb.INFO [2025-03-18 12:59:25.037][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-18 12:59:25.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:25.039][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:25.045][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-18 12:59:25.058][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:25.063][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:25.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:25.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:25.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:25.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:25.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:25.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:25.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:25.105][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.106][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.127][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.128][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.157][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.162][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.164][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.171][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.172][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.178][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.179][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.180][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.185][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.186][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.188][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.192][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:25.192][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.195][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:25.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.205][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.206][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.207][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.212][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:25.264][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:25.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.271][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.272][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.275][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:25.347][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-18 12:59:25.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.403][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:25.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:25.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:25.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:25.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.409][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:25.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:25.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.413][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:25.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:25.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.522][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.566][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:25.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.594][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.595][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.609][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.620][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.621][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.623][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.645][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.646][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.648][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.671][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.671][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.673][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.687][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.699][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.703][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.706][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.707][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.710][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.723][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.727][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.730][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.734][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.735][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.737][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.749][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.752][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.756][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.759][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.760][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.762][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.762][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.774][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.784][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.785][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.787][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.788][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.811][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.811][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.842][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.843][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.857][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:25.859][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:25.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.867][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:25.868][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:25.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.874][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:25.876][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:25.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.883][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:25.884][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:25.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.891][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.893][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:25.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.899][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.901][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:25.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.907][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.908][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:25.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.910][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.915][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.916][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:25.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.922][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.923][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:25.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.930][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:25.931][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:25.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:25.937][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:25.938][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:25.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:25.940][ef$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:25.948][biodb::testThat]
biodb.INFO [2025-03-18 12:59:25.949][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-18 12:59:25.950][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:25.951][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:25.965][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-18 12:59:25.974][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:25.980][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-18 12:59:25.981][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:25.982][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-18 12:59:25.984][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:26.016][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:26.017][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:26.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:26.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:26.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:26.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:26.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:26.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:26.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:26.032][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.033][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.035][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.056][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:26.058][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:26.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.061][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:26.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:26.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.065][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:26.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:26.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:26.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:26.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.072][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:26.073][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:26.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:26.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:26.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:26.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:26.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.081][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:26.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:26.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.086][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:26.087][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:26.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.089][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:26.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:26.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.093][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:26.094][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:26.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.095][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:26.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:26.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.100][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:26.101][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:26.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:26.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:26.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.107][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:26.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:26.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:26.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:26.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.122][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:26.123][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:26.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.126][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:26.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:26.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.129][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:26.130][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:26.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.132][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.133][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:26.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:26.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:26.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:26.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:26.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:26.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:26.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:26.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:26.171][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-18 12:59:26.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-18 12:59:26.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-18 12:59:26.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-18 12:59:26.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-18 12:59:26.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-18 12:59:26.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-18 12:59:26.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:26.191][biodb::testThat]
biodb.INFO [2025-03-18 12:59:26.192][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-18 12:59:26.193][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:26.194][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:26.197][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:26.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:26.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.200][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:26.201][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-18 12:59:26.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:26.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:26.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:26.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:26.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:26.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:26.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:26.249][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-18 12:59:26.255][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-18 12:59:26.276][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:26.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-18 12:59:26.293][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:26.295][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-18 12:59:26.319][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:26.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:26.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:26.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:26.728][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:28.604][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-03-18 12:59:28.607][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-18 12:59:28.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-18 12:59:28.627][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-18 12:59:28.630][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-18 12:59:28.648][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.650][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.652][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.654][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.666][ef$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:28.671][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.672][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-18 12:59:28.674][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:28.675][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:28.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:28.782][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:28.786][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:28.787][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-18 12:59:28.788][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:28.790][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-18 12:59:28.807][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.809][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-18 12:59:28.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:28.810][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:28.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:28.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:28.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:28.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:28.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:28.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:28.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:28.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:28.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:28.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:28.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:28.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.926][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:28.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.930][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:28.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:28.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.935][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:28.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:28.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:28.949][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.950][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-18 12:59:28.951][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:28.952][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.961][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.962][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-18 12:59:28.964][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:28.965][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.976][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.977][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-18 12:59:28.978][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:28.979][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:28.983][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-18 12:59:30.557][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-18 12:59:32.164][biodb::testThat]
biodb.INFO [2025-03-18 12:59:32.166][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-18 12:59:32.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:32.168][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:32.335][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-03-18 12:59:32.516][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:32.518][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:32.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:32.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:32.520][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:32.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:32.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:32.523][ef$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:32.525][biodb::testThat]
biodb.INFO [2025-03-18 12:59:32.526][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-18 12:59:32.527][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:32.528][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:32.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:32.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:32.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:32.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:32.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:32.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:32.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:32.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:32.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:32.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:32.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:32.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:32.657][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-03-18 12:59:32.660][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-03-18 12:59:32.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:32.676][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:32.692][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:32.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:33.257][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:33.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-18 12:59:33.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-18 12:59:33.358][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:33.362][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:33.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-18 12:59:33.365][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:33.367][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-18 12:59:33.384][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:33.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:33.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:33.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:33.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:33.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:33.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:33.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:33.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:33.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:33.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:33.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:33.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:33.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:33.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:33.434][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:33.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:33.439][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:33.440][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:33.544][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:33.647][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:33.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-18 12:59:33.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-18 12:59:33.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:33.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:33.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:33.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:33.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:33.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:33.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:33.670][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-18 12:59:33.727][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:33.729][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-18 12:59:33.731][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:33.732][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:33.733][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:33.734][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:33.735][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:33.735][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:33.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:33.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:33.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:33.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:33.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:33.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:33.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:33.749][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-18 12:59:33.752][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:33.753][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:33.754][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-18 12:59:33.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-18 12:59:33.967][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:33.970][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-18 12:59:33.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-18 12:59:33.978][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-18 12:59:33.980][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:33.981][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:33.982][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:33.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:33.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:33.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:33.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:33.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:33.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:33.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:33.996][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:33.997][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:33.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:33.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.004][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:34.005][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:34.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.017][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:34.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:34.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.021][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:34.022][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:34.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.025][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:34.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:34.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.028][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:34.029][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:34.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.031][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.035][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.036][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.038][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.042][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:34.043][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:34.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.046][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:34.047][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.048][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.049][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:34.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.053][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.054][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.059][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:34.060][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:34.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:34.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:34.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.066][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:34.067][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:34.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.069][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.070][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:34.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:34.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.073][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:34.074][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:34.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.076][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.077][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:34.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:34.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:34.120][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-18 12:59:34.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:34.142][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:34.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:34.147][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:34.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:34.248][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:34.361][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:34.364][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-18 12:59:34.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-18 12:59:34.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:34.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:34.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:34.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:34.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:34.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:34.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:34.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:34.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:34.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:34.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:34.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:34.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:34.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:34.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:34.465][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-18 12:59:34.466][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:34.468][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-18 12:59:34.469][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:34.470][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:34.471][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:34.472][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:34.473][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:34.474][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:34.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:34.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:34.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:34.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:34.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:34.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:34.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:34.500][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-18 12:59:34.503][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:34.504][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:34.506][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-18 12:59:34.652][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-18 12:59:34.738][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:34.741][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-18 12:59:34.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-18 12:59:34.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-18 12:59:34.749][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:34.751][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:34.752][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:34.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:34.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:34.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:34.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:34.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:34.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:34.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:34.777][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.779][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.780][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.785][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:34.786][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:34.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.788][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.793][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:34.794][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:34.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:34.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:34.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.801][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:34.802][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:34.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.804][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:34.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:34.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.810][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.811][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.812][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.813][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:34.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.817][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:34.818][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:34.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.821][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:34.822][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.825][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:34.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.828][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.829][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.831][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:34.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.835][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:34.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:34.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:34.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:34.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.843][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:34.844][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:34.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.846][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:34.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:34.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.850][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:34.850][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:34.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.853][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:34.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:34.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:34.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:34.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:34.897][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-18 12:59:34.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:34.928][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:34.932][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:34.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-18 12:59:34.934][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:34.936][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-18 12:59:34.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:34.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:34.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:34.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:34.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:34.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:34.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:34.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:34.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:34.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:34.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:34.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:34.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:34.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:34.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:34.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:34.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:34.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:34.979][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-18 12:59:34.980][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:34.982][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-18 12:59:34.983][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:34.984][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:34.985][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:34.986][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:34.987][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:34.989][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:34.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:34.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:34.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:35.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:35.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:35.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:35.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:35.005][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-18 12:59:35.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:35.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:35.011][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-18 12:59:35.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-18 12:59:35.217][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:35.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-18 12:59:35.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-18 12:59:35.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-18 12:59:35.228][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:35.229][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:35.230][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:35.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:35.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:35.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:35.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:35.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:35.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:35.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:35.245][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.246][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.248][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.252][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:35.253][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:35.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.256][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:35.257][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:35.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.270][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:35.271][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:35.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.274][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:35.275][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:35.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.278][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:35.279][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:35.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.282][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:35.283][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.285][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:35.286][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:35.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.288][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.289][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:35.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:35.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.292][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:35.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:35.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.297][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:35.298][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:35.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.301][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:35.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:35.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.304][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:35.305][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:35.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:35.343][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-18 12:59:35.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:35.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:35.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:35.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:35.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:35.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:35.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:35.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:35.381][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-18 12:59:35.382][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:35.383][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-18 12:59:35.385][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:35.385][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:35.386][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:35.387][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:35.388][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:35.389][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:35.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:35.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:35.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:35.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:35.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:35.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:35.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:35.402][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-18 12:59:35.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:35.406][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:35.407][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-18 12:59:35.530][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-18 12:59:35.619][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:35.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-18 12:59:35.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-18 12:59:35.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-18 12:59:35.630][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:35.631][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:35.632][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:35.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:35.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:35.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:35.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:35.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:35.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:35.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:35.647][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.648][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.655][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:35.655][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:35.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.658][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:35.659][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:35.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.672][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:35.673][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:35.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.675][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.676][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:35.677][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:35.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.678][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.679][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:35.680][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:35.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.682][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.683][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:35.684][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.685][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:35.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:35.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.690][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:35.691][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:35.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.693][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:35.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:35.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.698][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:35.698][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:35.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.700][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.701][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:35.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:35.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.705][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:35.705][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:35.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.707][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:35.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:35.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:35.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:35.742][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-18 12:59:35.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:35.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:35.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:35.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:35.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:35.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:35.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:35.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:35.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:35.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:35.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:35.778][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-18 12:59:35.779][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:35.781][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-18 12:59:35.782][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:35.783][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:35.784][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:35.785][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:35.785][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:35.786][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:35.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:35.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:35.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:35.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:35.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:35.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:35.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:35.800][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-18 12:59:35.802][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:35.803][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:35.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-18 12:59:35.901][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-18 12:59:35.987][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:35.990][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-18 12:59:35.994][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-18 12:59:35.997][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-18 12:59:35.999][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:36.000][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:36.001][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:36.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:36.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:36.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:36.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:36.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:36.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:36.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:36.016][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.017][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.018][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.023][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:36.024][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:36.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.038][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:36.039][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:36.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.042][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:36.043][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:36.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.046][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:36.047][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:36.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.048][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.050][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:36.050][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:36.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.053][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:36.054][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.057][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:36.058][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:36.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.061][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:36.062][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:36.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:36.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:36.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.069][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:36.070][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:36.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:36.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:36.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.076][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:36.076][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:36.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:36.113][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-18 12:59:36.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:36.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:36.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:36.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:36.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:36.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:36.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:36.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:36.152][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-18 12:59:36.153][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:36.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-18 12:59:36.156][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:36.157][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:36.158][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:36.159][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:36.160][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:36.161][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:36.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:36.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:36.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:36.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:36.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:36.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:36.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:36.176][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-18 12:59:36.179][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:36.180][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:36.182][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-18 12:59:36.283][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-18 12:59:36.385][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:36.388][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-18 12:59:36.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-18 12:59:36.395][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-18 12:59:36.396][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:36.398][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:36.399][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:36.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:36.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:36.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:36.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:36.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:36.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:36.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:36.413][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.415][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.427][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:36.432][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:36.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.434][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.436][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:36.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:36.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.439][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:36.440][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:36.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.442][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:36.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:36.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.447][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:36.448][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:36.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:36.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:36.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.454][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:36.455][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:36.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:36.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:36.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.461][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:36.462][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:36.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.464][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:36.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:36.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.467][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:36.468][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.471][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:36.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.475][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:36.475][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:36.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:36.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:36.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.481][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:36.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:36.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:36.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:36.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.489][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:36.490][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:36.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.492][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.493][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:36.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:36.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.497][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:36.498][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:36.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.499][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.501][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:36.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:36.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:36.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:36.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:36.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:36.545][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-18 12:59:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:36.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:36.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:36.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:36.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:36.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:36.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:36.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:36.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:36.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:36.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:36.569][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-18 12:59:36.570][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:36.571][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-18 12:59:36.572][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:36.573][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:36.574][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:36.575][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:36.576][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:36.577][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:36.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:36.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:36.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:36.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:36.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:36.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:36.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:36.591][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-18 12:59:36.594][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:36.596][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:36.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-18 12:59:37.138][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-18 12:59:37.234][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:37.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-18 12:59:37.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-18 12:59:37.254][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-18 12:59:37.256][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:37.257][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:37.258][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:37.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:37.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:37.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:37.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:37.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:37.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:37.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:37.272][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.273][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.281][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:37.282][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:37.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.284][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:37.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.288][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:37.289][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:37.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:37.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:37.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.295][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:37.296][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:37.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:37.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:37.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.302][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.303][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.309][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:37.310][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:37.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.312][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.313][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:37.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:37.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.316][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:37.317][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.319][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.320][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:37.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.324][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.331][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:37.332][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:37.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.333][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:37.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:37.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.346][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:37.347][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:37.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.349][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:37.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:37.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.355][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:37.356][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:37.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.360][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:37.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:37.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:37.398][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-18 12:59:37.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:37.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:37.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:37.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:37.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:37.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:37.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:37.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:37.422][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-18 12:59:37.423][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:37.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-18 12:59:37.426][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:37.437][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:37.438][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:37.440][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:37.441][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:37.442][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:37.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:37.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:37.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:37.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:37.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:37.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:37.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:37.459][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-18 12:59:37.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:37.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:37.465][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-18 12:59:37.570][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-18 12:59:37.661][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:37.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-18 12:59:37.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-18 12:59:37.670][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-18 12:59:37.672][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:37.673][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:37.674][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:37.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:37.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:37.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:37.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:37.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:37.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:37.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:37.689][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.690][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.692][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.696][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:37.697][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:37.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.699][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:37.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.704][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:37.704][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:37.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.706][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.707][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:37.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:37.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.711][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:37.711][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:37.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:37.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:37.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.718][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.719][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.720][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:37.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.735][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:37.737][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:37.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.739][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.741][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:37.742][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.743][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.745][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:37.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.748][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.750][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.752][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:37.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.759][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:37.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:37.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.762][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:37.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:37.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.767][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:37.767][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:37.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.770][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:37.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:37.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.773][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:37.775][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:37.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.778][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.779][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:37.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:37.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:37.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:37.818][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-18 12:59:37.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:37.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:37.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:37.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:37.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:37.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:37.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:37.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:37.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:37.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:37.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:37.849][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-18 12:59:37.850][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:37.851][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-18 12:59:37.853][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:37.854][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:37.855][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:37.856][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:37.856][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:37.857][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:37.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:37.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:37.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:37.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:37.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:37.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:37.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:37.871][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-18 12:59:37.874][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:37.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:37.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-18 12:59:37.972][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-18 12:59:38.076][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:38.079][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-18 12:59:38.083][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-18 12:59:38.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-18 12:59:38.087][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:38.088][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:38.089][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:38.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:38.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:38.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:38.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:38.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:38.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:38.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:38.103][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.104][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.112][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:38.113][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:38.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.115][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.116][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:38.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:38.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.356][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:38.356][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:38.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.357][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:38.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:38.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.360][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:38.361][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:38.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.364][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:38.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:38.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.368][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.369][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.373][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:38.373][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:38.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.375][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:38.375][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.376][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.377][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:38.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.378][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.379][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.379][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.381][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:38.382][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:38.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:38.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:38.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.384][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:38.385][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:38.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.386][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:38.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:38.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.387][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:38.387][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:38.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.388][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:38.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:38.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:38.423][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-18 12:59:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:38.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:38.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:38.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:38.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:38.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:38.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:38.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:38.447][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-18 12:59:38.448][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:38.450][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-18 12:59:38.451][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:38.452][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:38.454][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:38.455][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:38.456][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:38.457][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:38.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:38.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:38.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:38.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:38.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:38.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:38.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:38.471][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-18 12:59:38.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:38.473][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:38.474][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-18 12:59:38.573][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-18 12:59:38.658][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:38.660][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-18 12:59:38.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-18 12:59:38.666][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-18 12:59:38.668][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:38.669][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:38.670][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:38.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:38.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:38.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:38.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:38.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:38.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:38.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:38.681][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.682][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.682][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.685][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:38.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:38.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.687][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.688][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:38.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:38.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.690][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:38.690][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:38.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.691][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.692][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:38.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:38.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.694][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:38.694][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:38.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:38.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:38.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.698][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.698][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.699][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:38.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.701][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:38.701][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:38.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.703][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:38.703][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.704][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.704][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:38.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.706][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.707][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.707][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:38.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:38.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:38.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:38.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:38.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.716][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:38.716][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:38.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:38.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:38.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.719][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:38.720][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:38.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.720][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.721][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:38.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:38.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:38.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:38.740][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-18 12:59:38.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:38.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:38.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:38.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:38.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:38.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:38.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:38.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:38.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:38.755][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-18 12:59:38.756][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:38.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-18 12:59:38.757][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:38.757][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:38.759][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:38.761][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:38.762][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:38.763][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:38.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:38.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:38.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:38.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:38.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:38.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:38.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:38.788][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-18 12:59:38.792][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:38.793][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:38.794][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-18 12:59:38.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-18 12:59:38.974][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:38.976][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-18 12:59:38.978][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-18 12:59:38.979][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-18 12:59:38.980][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:38.981][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:38.981][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:38.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:38.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:38.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:38.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:38.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:38.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:38.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:38.991][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.992][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:38.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:38.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:38.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:38.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.000][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:39.001][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:39.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.003][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:39.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:39.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.007][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:39.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:39.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.009][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:39.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:39.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.014][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:39.015][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:39.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:39.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:39.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.022][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.022][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.026][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:39.026][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:39.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.027][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:39.028][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.029][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:39.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.033][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.041][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:39.042][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:39.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.043][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:39.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:39.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.048][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:39.049][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:39.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.051][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.052][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:39.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:39.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.056][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:39.057][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:39.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.060][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:39.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:39.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:39.084][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-18 12:59:39.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:39.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:39.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:39.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:39.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:39.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:39.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:39.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:39.099][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-18 12:59:39.100][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:39.100][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-18 12:59:39.101][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:39.101][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:39.102][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:39.102][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:39.102][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:39.103][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:39.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:39.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:39.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:39.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:39.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:39.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:39.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:39.112][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-18 12:59:39.113][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:39.114][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:39.114][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-18 12:59:39.414][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-18 12:59:39.501][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:39.504][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-18 12:59:39.508][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-18 12:59:39.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-18 12:59:39.512][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:39.513][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:39.515][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:39.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:39.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:39.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:39.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:39.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:39.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:39.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:39.532][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.534][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.542][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:39.543][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:39.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.545][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:39.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:39.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:39.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:39.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:39.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:39.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.559][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:39.560][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:39.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:39.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:39.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.568][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.569][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.570][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:39.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.575][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:39.577][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:39.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.582][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:39.584][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.587][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:39.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.591][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.592][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:39.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.598][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:39.599][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:39.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:39.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:39.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.607][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:39.608][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:39.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.610][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.612][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:39.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:39.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.617][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:39.618][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:39.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:39.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:39.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:39.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:39.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:39.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:39.677][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-18 12:59:39.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:39.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:39.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:39.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:39.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:39.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:39.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:39.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:39.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:39.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:39.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:39.698][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-18 12:59:39.699][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:39.701][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-18 12:59:39.702][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:39.703][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:39.704][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:39.705][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:39.706][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:39.706][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:39.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:39.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:39.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:39.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:39.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:39.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:39.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:39.720][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-18 12:59:39.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:39.724][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:39.726][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-18 12:59:40.022][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-18 12:59:40.122][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:40.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-18 12:59:40.130][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-18 12:59:40.133][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-18 12:59:40.135][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:40.136][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:40.137][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:40.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:40.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:40.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:40.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:40.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:40.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:40.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:40.151][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.152][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.158][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:40.159][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:40.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.162][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:40.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:40.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.166][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:40.167][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:40.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.169][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:40.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:40.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.172][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:40.173][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:40.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.176][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:40.177][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:40.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.178][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.179][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:40.180][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:40.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.183][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:40.184][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.185][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.186][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:40.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.190][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:40.191][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:40.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.192][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:40.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:40.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.197][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:40.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:40.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:40.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:40.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.204][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:40.205][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:40.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.207][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.208][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:40.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:40.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.212][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:40.213][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:40.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:40.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:40.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:40.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:40.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:40.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:40.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:40.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:40.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:40.251][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-18 12:59:40.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:40.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:40.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:40.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:40.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:40.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:40.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:40.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:40.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:40.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:40.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:40.272][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-18 12:59:40.273][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:40.275][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-18 12:59:40.276][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:40.277][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:40.278][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:40.279][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:40.279][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:40.280][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:40.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:40.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:40.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:40.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:40.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:40.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:40.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:40.293][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-18 12:59:40.296][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:40.297][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:40.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-18 12:59:41.395][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-18 12:59:41.493][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:41.497][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-18 12:59:41.502][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-18 12:59:41.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-18 12:59:41.506][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:41.508][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:41.509][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:41.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:41.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:41.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:41.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:41.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:41.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:41.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:41.525][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.526][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.528][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.533][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:41.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:41.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.536][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.537][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:41.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:41.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.542][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:41.543][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:41.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:41.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:41.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.551][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:41.552][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:41.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.555][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:41.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:41.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.559][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:41.560][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:41.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.562][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:41.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.566][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:41.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:41.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:41.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.572][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:41.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:41.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.576][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:41.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:41.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.579][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:41.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:41.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.583][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:41.584][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:41.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.587][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:41.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:41.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.604][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:41.605][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:41.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:41.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:41.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:41.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:41.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:41.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:41.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:41.645][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-18 12:59:41.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:41.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:41.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:41.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:41.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:41.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:41.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:41.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:41.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:41.667][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-18 12:59:41.668][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:41.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-18 12:59:41.670][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:41.671][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:41.672][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:41.673][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:41.674][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:41.675][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:41.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:41.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:41.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:41.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:41.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:41.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:41.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:41.689][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-18 12:59:41.692][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:41.693][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:41.695][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-18 12:59:41.807][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-18 12:59:41.924][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:41.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-18 12:59:41.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-18 12:59:41.934][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-18 12:59:41.939][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:41.940][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:41.942][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:41.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:41.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:41.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:41.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:41.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:41.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:41.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:41.957][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.958][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.960][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:41.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:41.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.965][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:41.966][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:41.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.968][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.969][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:41.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:41.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.972][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:41.973][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:41.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.976][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:41.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:41.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.979][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:41.980][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:41.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:41.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:41.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.988][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:41.989][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:41.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:41.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:41.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:41.996][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:41.997][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:41.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:41.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.000][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:42.001][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.004][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:42.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.007][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.008][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.011][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.017][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:42.018][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:42.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:42.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:42.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.027][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:42.028][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:42.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.030][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:42.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:42.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.034][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:42.035][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:42.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.037][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:42.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:42.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:42.074][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-18 12:59:42.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:42.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:42.097][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-18 12:59:42.098][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:42.100][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-18 12:59:42.101][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:42.102][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:42.103][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:42.104][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:42.105][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:42.106][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:42.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:42.120][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-18 12:59:42.123][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:42.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:42.125][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-18 12:59:42.222][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-18 12:59:42.315][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:42.319][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-18 12:59:42.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-18 12:59:42.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-18 12:59:42.328][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:42.330][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:42.331][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:42.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:42.345][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.346][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.353][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:42.354][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:42.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.356][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:42.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:42.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.362][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:42.364][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:42.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:42.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:42.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.370][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:42.371][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:42.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.386][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:42.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.392][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.394][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.400][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:42.401][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:42.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.404][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:42.405][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.406][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.407][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:42.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.411][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.411][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.421][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:42.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:42.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.424][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:42.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:42.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.432][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:42.435][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:42.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.438][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:42.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:42.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.442][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:42.443][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:42.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.445][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.446][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:42.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:42.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:42.482][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-18 12:59:42.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:42.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:42.504][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-18 12:59:42.505][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:42.506][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-18 12:59:42.507][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:42.508][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:42.509][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:42.510][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:42.511][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:42.512][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:42.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:42.531][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-18 12:59:42.535][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:42.536][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:42.538][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-18 12:59:42.652][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-18 12:59:42.756][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:42.758][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-18 12:59:42.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-18 12:59:42.766][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-18 12:59:42.768][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:42.769][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:42.771][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:42.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:42.785][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.786][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.788][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.792][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:42.793][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:42.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.796][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:42.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:42.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.799][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:42.800][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:42.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.802][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.803][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:42.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:42.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.807][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:42.808][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:42.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:42.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:42.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.813][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.814][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.816][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:42.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.820][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:42.821][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:42.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.824][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:42.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.827][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.830][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:42.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.834][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.835][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:42.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.841][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:42.842][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:42.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:42.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:42.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.848][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:42.849][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:42.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.850][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.852][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:42.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:42.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.856][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:42.857][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:42.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.863][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:42.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:42.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:42.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:42.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:42.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:42.905][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-18 12:59:42.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:42.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:42.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:42.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:42.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:42.930][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-18 12:59:42.931][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:42.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-18 12:59:42.934][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:42.936][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:42.937][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:42.938][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:42.939][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:42.939][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:42.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:42.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:42.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:42.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:42.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:42.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:42.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:42.953][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-18 12:59:42.956][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:42.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:42.969][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-18 12:59:43.067][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-18 12:59:43.157][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:43.160][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-18 12:59:43.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-18 12:59:43.167][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-18 12:59:43.168][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:43.169][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:43.170][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:43.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:43.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:43.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:43.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:43.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:43.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:43.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:43.189][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.190][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.192][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.197][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:43.198][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:43.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.200][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.201][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.205][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:43.206][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:43.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.208][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:43.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:43.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.214][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:43.215][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:43.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.216][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:43.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:43.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.221][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.222][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.224][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.229][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:43.229][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:43.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.232][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:43.233][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.236][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:43.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.240][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.241][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.247][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:43.248][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:43.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.249][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:43.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:43.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.254][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:43.255][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:43.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.256][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.258][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:43.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:43.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.261][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:43.262][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:43.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.265][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:43.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:43.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:43.310][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-18 12:59:43.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:43.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:43.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:43.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:43.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:43.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:43.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:43.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:43.332][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-18 12:59:43.333][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:43.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-18 12:59:43.336][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:43.337][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:43.338][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:43.339][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:43.340][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:43.340][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:43.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:43.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:43.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:43.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:43.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:43.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:43.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:43.354][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-18 12:59:43.357][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:43.358][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:43.360][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-18 12:59:43.463][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-18 12:59:43.549][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:43.552][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-18 12:59:43.556][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-18 12:59:43.559][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-18 12:59:43.561][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:43.563][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:43.564][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:43.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:43.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:43.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:43.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:43.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:43.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:43.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:43.583][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.584][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.590][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:43.591][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:43.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.594][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:43.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.598][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:43.599][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:43.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.601][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:43.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:43.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.605][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:43.606][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:43.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:43.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:43.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.613][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.614][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.616][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:43.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.621][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:43.621][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:43.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.624][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:43.625][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.627][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.628][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:43.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.632][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:43.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.638][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:43.639][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:43.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:43.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:43.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.645][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:43.646][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:43.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.648][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.649][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:43.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.652][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:43.653][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:43.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.656][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:43.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:43.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:43.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:43.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:43.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:43.705][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-18 12:59:43.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:43.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:43.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:43.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:43.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:43.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:43.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:43.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:43.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:43.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:43.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:43.730][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-18 12:59:43.731][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:43.735][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-18 12:59:43.736][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:43.737][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:43.738][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:43.739][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:43.740][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:43.740][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:43.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:43.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:43.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:43.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:43.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:43.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:43.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:43.758][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-18 12:59:43.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:43.761][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:43.763][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-18 12:59:44.082][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-18 12:59:44.176][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:44.178][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-18 12:59:44.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-18 12:59:44.185][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-18 12:59:44.186][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:44.187][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:44.188][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:44.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:44.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:44.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:44.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:44.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:44.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:44.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:44.203][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.204][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.206][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.211][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:44.212][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:44.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.213][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.214][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:44.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:44.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.218][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:44.219][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:44.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.222][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:44.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:44.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:44.227][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:44.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:44.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:44.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.233][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.234][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.236][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.240][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:44.242][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:44.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.244][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:44.245][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.247][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.248][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:44.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.251][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.258][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:44.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:44.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:44.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:44.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:44.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:44.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.269][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:44.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:44.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.272][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:44.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:44.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.274][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.275][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:44.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:44.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:44.312][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-18 12:59:44.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:44.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:44.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:44.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:44.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:44.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:44.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:44.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:44.333][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-18 12:59:44.334][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:44.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-18 12:59:44.336][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:44.337][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:44.338][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:44.339][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:44.340][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:44.341][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:44.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:44.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:44.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:44.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:44.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:44.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:44.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:44.355][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-18 12:59:44.358][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:44.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:44.360][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-18 12:59:44.710][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-18 12:59:44.805][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:44.807][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-18 12:59:44.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-18 12:59:44.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-18 12:59:44.816][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:44.818][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:44.819][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:44.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:44.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:44.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:44.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:44.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:44.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:44.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:44.837][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.847][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:44.848][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:44.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.850][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.852][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:44.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:44.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.857][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:44.858][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:44.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.861][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:44.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:44.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.865][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:44.866][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:44.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:44.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:44.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.872][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.873][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:44.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.879][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:44.880][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:44.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.881][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.882][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:44.883][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.886][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:44.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.889][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.890][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:44.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.896][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:44.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:44.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.911][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:44.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:44.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.916][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:44.917][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:44.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.918][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.919][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:44.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:44.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.923][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:44.924][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:44.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.926][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:44.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:44.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:44.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:44.962][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-18 12:59:44.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:44.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:44.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:44.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:44.993][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:44.997][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:44.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-18 12:59:45.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:45.001][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-18 12:59:45.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:45.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:45.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:45.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:45.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:45.516][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:45.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:45.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:45.523][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:45.618][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:45.718][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:45.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-18 12:59:45.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-18 12:59:45.730][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:45.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:45.735][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:45.737][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:45.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:45.918][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:45.920][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-18 12:59:45.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-18 12:59:45.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:45.939][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-18 12:59:45.940][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:45.941][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-18 12:59:45.943][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:45.944][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:45.945][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:45.946][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:45.946][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:45.947][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:45.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:45.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:45.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:45.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:45.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:45.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:45.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:45.961][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-18 12:59:45.977][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:45.978][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:45.980][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-18 12:59:46.279][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-18 12:59:46.384][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:46.387][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-18 12:59:46.391][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-18 12:59:46.393][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-18 12:59:46.395][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:46.396][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:46.397][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:46.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:46.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:46.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:46.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:46.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:46.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:46.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:46.415][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.416][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.417][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.422][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:46.423][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:46.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.424][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.426][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:46.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:46.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.429][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:46.431][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:46.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.435][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:46.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:46.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.439][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:46.440][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:46.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.442][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:46.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:46.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.446][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.447][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.453][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:46.454][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:46.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.457][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:46.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:46.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.460][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:46.461][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:46.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.462][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.463][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:46.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:46.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.467][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.468][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.474][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:46.474][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:46.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:46.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:46.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.481][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:46.482][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:46.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.483][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.484][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:46.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.488][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:46.488][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:46.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.490][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:46.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:46.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:46.533][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-18 12:59:46.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:46.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:46.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:46.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:46.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:46.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:46.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:46.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:46.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:46.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:46.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:46.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:46.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:46.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:46.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:46.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:46.577][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-18 12:59:46.579][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:46.583][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-18 12:59:46.585][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:46.585][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:46.586][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:46.587][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:46.588][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:46.588][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:46.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:46.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:46.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:46.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:46.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:46.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:46.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:46.602][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-18 12:59:46.605][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:46.606][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:46.607][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-18 12:59:46.703][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-18 12:59:46.795][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:46.798][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-18 12:59:46.802][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-18 12:59:46.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-18 12:59:46.807][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:46.808][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:46.809][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:46.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:46.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:46.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:46.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:46.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:46.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:46.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:46.822][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.823][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.825][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.830][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:46.830][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:46.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.832][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.833][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:46.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:46.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.836][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:46.837][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:46.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:46.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:46.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.843][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:46.844][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:46.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:46.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:46.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.850][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.851][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:46.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.856][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:46.857][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:46.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.860][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:46.861][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:46.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.862][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.863][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:46.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:46.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.867][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.867][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.875][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:46.877][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:46.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:46.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:46.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.884][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:46.885][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:46.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.887][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:46.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:46.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.891][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:46.892][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:46.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.896][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:46.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:46.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:46.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:46.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:46.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:46.953][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-18 12:59:46.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:46.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:46.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:46.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:46.984][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:46.988][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:46.990][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-18 12:59:46.991][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:46.992][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-18 12:59:46.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:46.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:46.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.505][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:47.509][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:47.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-18 12:59:47.514][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:47.516][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-18 12:59:47.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:47.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:47.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:47.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:47.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:47.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:47.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:47.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:47.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:47.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:47.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:47.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:48.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.027][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:48.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:48.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:48.048][biodb::testThat]
biodb.INFO [2025-03-18 12:59:48.050][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-18 12:59:48.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:48.053][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:48.056][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:48.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:48.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:48.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:48.092][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:48.096][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:48.097][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-18 12:59:48.098][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:48.100][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-18 12:59:48.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:48.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:48.127][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:48.131][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:48.132][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-18 12:59:48.133][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:48.135][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-18 12:59:48.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:48.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:48.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:48.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:48.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:48.182][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-18 12:59:48.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:48.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.202][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.203][private$selectFields]
biodb.TRACE[2025-03-18 12:59:48.204][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:48.204][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:48.205][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.206][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.207][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.211][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.213][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.215][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.216][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.220][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:48.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.242][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-18 12:59:48.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:48.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.263][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.265][private$selectFields]
biodb.TRACE[2025-03-18 12:59:48.266][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:48.267][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:48.268][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.269][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.270][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.272][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.275][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.276][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.280][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:48.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.293][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-18 12:59:48.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:48.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.312][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.314][private$selectFields]
biodb.TRACE[2025-03-18 12:59:48.315][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:48.316][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:48.317][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.318][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.319][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.321][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.322][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.323][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.325][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.326][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:48.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.327][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.330][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:48.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:48.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.341][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-18 12:59:48.343][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-18 12:59:48.344][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-18 12:59:48.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:48.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:48.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:48.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:48.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:48.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:48.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:48.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:48.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:48.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:48.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:48.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:48.453][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:48.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:48.456][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:48.547][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:48.642][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:48.645][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-18 12:59:48.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-18 12:59:48.653][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:48.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:48.658][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:48.659][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:48.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:49.040][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:49.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-18 12:59:49.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-18 12:59:49.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.145][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-18 12:59:49.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.187][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.188][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.188][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.189][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.190][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.191][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.192][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.194][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.195][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.197][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.198][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.199][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.200][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.202][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.203][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.214][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-18 12:59:49.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.265][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.266][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.267][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.268][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.269][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.270][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.271][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.273][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.274][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.276][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.277][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.301][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.303][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.304][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.306][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-18 12:59:49.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.338][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.339][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.340][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.340][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.341][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.342][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.345][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.349][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.350][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.351][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.352][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.355][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.366][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-18 12:59:49.367][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-18 12:59:49.368][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-18 12:59:49.377][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:49.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:49.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:49.385][biodb::testThat]
biodb.INFO [2025-03-18 12:59:49.386][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-18 12:59:49.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:49.387][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:49.390][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:49.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:49.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:49.423][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:49.427][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:49.428][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-18 12:59:49.429][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:49.430][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-18 12:59:49.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.454][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:49.457][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:49.459][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-18 12:59:49.460][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:49.461][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-18 12:59:49.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.506][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-18 12:59:49.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.525][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.526][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.527][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.528][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.529][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.530][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.534][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.536][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.537][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.537][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.538][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.540][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.541][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.552][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-18 12:59:49.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.571][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.571][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.572][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.573][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.574][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.575][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.578][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.579][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.580][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.581][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.583][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.585][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.596][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-18 12:59:49.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.614][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.615][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.616][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.617][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.617][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.619][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.628][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.629][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.630][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.632][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.632][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.633][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.634][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.635][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.636][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.637][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.648][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-18 12:59:49.649][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-18 12:59:49.650][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-18 12:59:49.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:49.688][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:49.692][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:49.693][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-18 12:59:49.694][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:49.696][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-18 12:59:49.700][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:49.703][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:49.704][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-18 12:59:49.706][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:49.708][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-18 12:59:49.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:49.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.775][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-18 12:59:49.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.793][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.794][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.795][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.796][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.796][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.797][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.798][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.800][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.801][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.803][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.804][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.805][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.806][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.807][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.808][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.819][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-18 12:59:49.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.838][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.838][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.839][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.840][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.841][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.842][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.849][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.850][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.852][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.853][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.854][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.865][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-18 12:59:49.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:49.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.884][private$selectFields]
biodb.TRACE[2025-03-18 12:59:49.884][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:49.885][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:49.886][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.887][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.888][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.891][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.891][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.894][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.895][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:49.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.898][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.899][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:49.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:49.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.909][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-18 12:59:49.910][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-18 12:59:49.911][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-18 12:59:49.920][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:49.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:49.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:49.928][biodb::testThat]
biodb.INFO [2025-03-18 12:59:49.929][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-18 12:59:49.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:49.931][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:49.935][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:49.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:49.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:49.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:49.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:49.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:49.979][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:49.983][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:49.984][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-18 12:59:49.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:49.987][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-18 12:59:49.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:49.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:49.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:49.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:49.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:49.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:49.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.011][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:50.015][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:50.016][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-18 12:59:50.017][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:50.019][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-18 12:59:50.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.066][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-18 12:59:50.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.087][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.088][private$selectFields]
biodb.TRACE[2025-03-18 12:59:50.089][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:50.089][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:50.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.098][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.102][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:50.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.114][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-18 12:59:50.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.132][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.133][private$selectFields]
biodb.TRACE[2025-03-18 12:59:50.133][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:50.134][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:50.135][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.136][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.139][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.140][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.141][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.142][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.143][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.144][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.147][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.158][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-18 12:59:50.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.178][private$selectFields]
biodb.TRACE[2025-03-18 12:59:50.179][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:50.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:50.181][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.182][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.182][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.184][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.186][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.188][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.189][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.189][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.190][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.192][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.193][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:50.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.203][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-18 12:59:50.204][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-18 12:59:50.205][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-18 12:59:50.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:50.256][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:50.259][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:50.261][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-18 12:59:50.262][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:50.263][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-18 12:59:50.266][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:50.269][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:50.270][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-18 12:59:50.271][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:50.272][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-18 12:59:50.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.345][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-18 12:59:50.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.365][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.366][private$selectFields]
biodb.TRACE[2025-03-18 12:59:50.367][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:50.368][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:50.368][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.369][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.370][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.372][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.372][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.373][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.375][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.376][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.376][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.377][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.378][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.381][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:50.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.393][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-18 12:59:50.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.414][private$selectFields]
biodb.TRACE[2025-03-18 12:59:50.414][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:50.415][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:50.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.417][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.420][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.422][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.423][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.424][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.425][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.425][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.427][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.428][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:50.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.438][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-18 12:59:50.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.457][private$selectFields]
biodb.TRACE[2025-03-18 12:59:50.458][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-18 12:59:50.459][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-18 12:59:50.460][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.462][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.465][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.466][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.468][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.469][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-18 12:59:50.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.474][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-18 12:59:50.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.485][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-18 12:59:50.486][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-18 12:59:50.487][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-18 12:59:50.507][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:50.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-18 12:59:50.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:50.515][biodb::testThat]
biodb.INFO [2025-03-18 12:59:50.516][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-18 12:59:50.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:50.518][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:50.519][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-18 12:59:50.520][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:50.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-18 12:59:50.523][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:50.524][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:50.525][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:50.526][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:50.527][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:50.528][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:50.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:50.542][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-18 12:59:50.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:50.546][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:50.548][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-18 12:59:50.766][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-18 12:59:50.859][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:50.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-18 12:59:50.865][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-18 12:59:50.868][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-18 12:59:50.869][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:50.870][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:50.871][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:50.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:50.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:50.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:50.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:50.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:50.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:50.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:50.884][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.885][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.887][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.893][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:50.894][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:50.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.897][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:50.898][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:50.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.899][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.900][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:50.901][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:50.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.904][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:50.905][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:50.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.907][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:50.908][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:50.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.910][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.911][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:50.912][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:50.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.914][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.915][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.915][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:50.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.918][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.919][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:50.920][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:50.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.923][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:50.925][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:50.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.928][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:50.929][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:50.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.930][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:50.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:50.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:50.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:50.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:50.978][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-18 12:59:50.978][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-18 12:59:50.987][biodb::testThat]
biodb.INFO [2025-03-18 12:59:50.988][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-18 12:59:50.989][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:50.989][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:51.000][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-18 12:59:51.002][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-18 12:59:51.003][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-18 12:59:51.004][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-18 12:59:51.006][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-18 12:59:51.007][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:51.007][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:51.008][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:51.009][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:51.010][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:51.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:51.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:51.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:51.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:51.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:51.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:51.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:51.025][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-18 12:59:51.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:51.028][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:51.030][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-18 12:59:51.121][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-18 12:59:51.430][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:51.433][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-18 12:59:51.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-18 12:59:51.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:51.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:51.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:51.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:51.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:51.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:51.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:51.449][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-18 12:59:51.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:51.452][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:51.453][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-18 12:59:51.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-18 12:59:52.673][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:52.675][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-18 12:59:52.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-18 12:59:52.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:52.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:52.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:52.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:52.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:52.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:52.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:52.683][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-18 12:59:52.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:52.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:52.686][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-18 12:59:52.768][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-18 12:59:52.863][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:52.866][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-18 12:59:52.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-18 12:59:52.873][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-18 12:59:52.875][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 12:59:52.876][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-18 12:59:52.877][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-18 12:59:52.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:52.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:52.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:52.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:52.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:52.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:52.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:52.891][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.892][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.899][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:52.900][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:52.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.903][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:52.904][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:52.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.905][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.906][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:52.907][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:52.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.910][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:52.911][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:52.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.914][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:52.914][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:52.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.917][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:52.918][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:52.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.920][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:52.921][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:52.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.923][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:52.924][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:52.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.926][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:52.927][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:52.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.929][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.930][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:52.931][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:52.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:52.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:52.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:52.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:52.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:52.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:52.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:52.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:52.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:52.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:52.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:52.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:52.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:52.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:52.972][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:52.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:52.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.980][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:52.981][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:52.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.984][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:52.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:52.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.988][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:52.989][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:52.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.992][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:52.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:52.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.996][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:52.997][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:52.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:52.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:52.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:53.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:53.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.003][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.004][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.009][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.010][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.013][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.016][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:53.017][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:53.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.019][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.024][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.025][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.030][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:53.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:53.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.032][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:53.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:53.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.036][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:53.037][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:53.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:53.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:53.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.043][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:53.044][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:53.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.047][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:53.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:53.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:53.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:53.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:53.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:53.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:53.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:53.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:53.101][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.102][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.107][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:53.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:53.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.111][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 12:59:53.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 12:59:53.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.114][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:53.115][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:53.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:53.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:53.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.122][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:53.123][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:53.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.125][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:53.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:53.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.129][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.130][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.132][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:53.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.136][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.137][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.140][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:53.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.143][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:53.144][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:53.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.147][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 12:59:53.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 12:59:53.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.152][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.157][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:53.158][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:53.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:53.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:53.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.164][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:53.165][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:53.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.168][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 12:59:53.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 12:59:53.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:53.172][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:53.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:53.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:53.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:53.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:53.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:53.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:53.230][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-18 12:59:53.230][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-18 12:59:53.231][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-18 12:59:53.245][biodb::testThat]
biodb.INFO [2025-03-18 12:59:53.246][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-18 12:59:53.247][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:53.248][biodb::testThat]
biodb.INFO [2025-03-18 12:59:53.273][biodb::testThat]
biodb.INFO [2025-03-18 12:59:53.274][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-18 12:59:53.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:53.276][biodb::testThat]
biodb.INFO [2025-03-18 12:59:53.285][biodb::testThat]
biodb.INFO [2025-03-18 12:59:53.286][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-18 12:59:53.287][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:53.288][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:53.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:53.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:53.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:53.297][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:53.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:53.721][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:53.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-18 12:59:53.729][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-18 12:59:53.743][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:53.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:53.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:53.747][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:53.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:53.750][ef$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:53.752][biodb::testThat]
biodb.INFO [2025-03-18 12:59:53.752][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-18 12:59:53.753][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:53.754][biodb::testThat]
biodb.ERROR[2025-03-18 12:59:53.769][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-18 12:59:53.787][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-18 12:59:53.802][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-18 12:59:53.804][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-18 12:59:53.805][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-18 12:59:53.806][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-18 12:59:53.806][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:53.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:53.808][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:53.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:53.809][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-18 12:59:53.821][biodb::testContext]
biodb.INFO [2025-03-18 12:59:53.822][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:53.823][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-18 12:59:53.823][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:53.824][biodb::testContext]
biodb.INFO [2025-03-18 12:59:53.826][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:53.828][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:53.845][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:53.846][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-18 12:59:53.847][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-18 12:59:53.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.850][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-18 12:59:53.851][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-18 12:59:53.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.854][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-18 12:59:53.855][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-18 12:59:53.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.858][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-18 12:59:53.858][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-18 12:59:53.859][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-18 12:59:53.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.862][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-18 12:59:53.863][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-18 12:59:53.864][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-18 12:59:53.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.867][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-18 12:59:53.867][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-18 12:59:53.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.870][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-18 12:59:53.871][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-18 12:59:53.872][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-18 12:59:53.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.875][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-18 12:59:53.876][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-18 12:59:53.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.878][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-18 12:59:53.879][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-18 12:59:53.880][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-18 12:59:53.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.883][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:53.884][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-18 12:59:53.885][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-18 12:59:53.885][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-18 12:59:53.886][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-18 12:59:53.887][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-18 12:59:53.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.890][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-18 12:59:53.891][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-18 12:59:53.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.894][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-18 12:59:53.895][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-18 12:59:53.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.897][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-18 12:59:53.898][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-18 12:59:53.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.901][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-18 12:59:53.902][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-18 12:59:53.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.905][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-18 12:59:53.906][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-18 12:59:53.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.908][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:53.909][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-18 12:59:53.926][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-18 12:59:53.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.930][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-18 12:59:53.931][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-18 12:59:53.932][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-18 12:59:53.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:53.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:53.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:53.935][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-18 12:59:53.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.937][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-18 12:59:53.938][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.939][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:53.940][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.941][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.942][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.942][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.943][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:53.944][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:53.945][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.946][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-18 12:59:53.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:53.947][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:53.948][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.949][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:53.949][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:53.949][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:53.949][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:53.949][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:53.950][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:53.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:53.951][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:53.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:53.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:53.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:53.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.955][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:53.956][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:53.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:53.958][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.958][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:53.959][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-18 12:59:53.961][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.962][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:53.963][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.964][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:53.964][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.966][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.967][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.968][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.969][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:53.970][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:53.971][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.972][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-18 12:59:53.973][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:53.974][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:53.975][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.976][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:53.976][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:53.976][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:53.976][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:53.976][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:53.977][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:53.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:53.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:53.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:53.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:53.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:53.981][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.982][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:53.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:53.984][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:53.984][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.985][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:53.986][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-18 12:59:53.988][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.989][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-18 12:59:53.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.990][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:53.991][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:53.992][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.993][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:53.994][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:53.995][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:53.996][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:53.997][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-18 12:59:53.998][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:53.998][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:53.999][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.000][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:54.001][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:54.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:54.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:54.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:54.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:54.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:54.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:54.006][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:54.007][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:54.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:54.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:54.009][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:54.010][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-18 12:59:54.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:54.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:54.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:54.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:54.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:54.018][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:54.018][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:54.019][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:54.020][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-18 12:59:54.021][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:54.021][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:54.022][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.023][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:54.024][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:54.024][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:54.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:54.026][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:54.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:54.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:54.028][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:54.029][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:54.030][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:54.030][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:54.031][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:54.032][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:54.033][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:54.034][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.094][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-18 12:59:54.096][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-18 12:59:54.097][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-18 12:59:54.098][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-18 12:59:54.099][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:54.100][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:54.101][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:54.102][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:54.104][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-18 12:59:54.105][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:54.106][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:54.107][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-18 12:59:54.108][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:54.109][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:54.110][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-18 12:59:54.111][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:54.113][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-18 12:59:54.114][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-18 12:59:54.115][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:54.116][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-18 12:59:54.117][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-18 12:59:54.118][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-18 12:59:54.119][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-18 12:59:54.120][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-18 12:59:54.122][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-18 12:59:54.123][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-18 12:59:54.124][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-18 12:59:54.125][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-18 12:59:54.126][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-18 12:59:54.127][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-18 12:59:54.128][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-18 12:59:54.129][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-18 12:59:54.138][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-18 12:59:54.139][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-18 12:59:54.140][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-18 12:59:54.142][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-18 12:59:54.143][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-18 12:59:54.144][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-18 12:59:54.145][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-18 12:59:54.146][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-18 12:59:54.147][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-18 12:59:54.148][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-18 12:59:54.149][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-18 12:59:54.151][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-18 12:59:54.152][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-18 12:59:54.154][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-18 12:59:54.155][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-18 12:59:54.157][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-18 12:59:54.158][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-18 12:59:54.159][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-18 12:59:54.160][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-18 12:59:54.162][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-18 12:59:54.163][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-18 12:59:54.164][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-18 12:59:54.165][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-18 12:59:54.167][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-18 12:59:54.168][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-18 12:59:54.169][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-18 12:59:54.170][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-18 12:59:54.172][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-18 12:59:54.173][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-18 12:59:54.174][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-18 12:59:54.175][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-18 12:59:54.176][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-18 12:59:54.177][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-18 12:59:54.179][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-18 12:59:54.180][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:54.181][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:54.182][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-18 12:59:54.183][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-18 12:59:54.184][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-18 12:59:54.186][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-18 12:59:54.187][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-18 12:59:54.188][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-18 12:59:54.189][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-18 12:59:54.190][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-18 12:59:54.192][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-18 12:59:54.193][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-18 12:59:54.194][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-18 12:59:54.195][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-18 12:59:54.196][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-18 12:59:54.197][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-18 12:59:54.198][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-18 12:59:54.200][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-18 12:59:54.201][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:54.202][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:54.203][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.205][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:54.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.300][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:54.302][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-18 12:59:54.304][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:54.305][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-18 12:59:54.305][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.306][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:54.307][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:54.309][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.310][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-18 12:59:54.310][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-18 12:59:54.311][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:54.312][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.314][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-18 12:59:54.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-18 12:59:54.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-18 12:59:54.317][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:54.318][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:54.318][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:54.318][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:54.318][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-18 12:59:54.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:54.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:54.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:54.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:54.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:54.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:54.324][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:54.324][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-18 12:59:54.325][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:54.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:54.326][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:54.327][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-18 12:59:54.327][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-18 12:59:54.333][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:54.335][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:54.337][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-18 12:59:54.338][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:54.339][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:54.341][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:54.344][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-18 12:59:54.345][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-18 12:59:54.346][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-18 12:59:54.348][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-18 12:59:54.349][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:54.349][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:54.351][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-18 12:59:54.351][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-18 12:59:54.353][biodb::testThat]
biodb.INFO [2025-03-18 12:59:54.354][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-18 12:59:54.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:54.355][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:54.359][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-18 12:59:54.363][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:54.365][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:54.366][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-18 12:59:54.447][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-18 12:59:54.576][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:54.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-18 12:59:54.582][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-18 12:59:54.586][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:54.590][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:54.590][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:54.592][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:54.673][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:54.763][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:54.765][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-18 12:59:54.768][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-18 12:59:54.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:54.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:54.777][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:54.777][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:54.778][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:54.860][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:54.946][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:54.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-18 12:59:54.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-18 12:59:54.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:54.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:54.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:54.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:54.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:54.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:54.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:54.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:54.994][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:54.997][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:54.999][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-18 12:59:55.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:55.001][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-18 12:59:55.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:55.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:55.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:55.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:55.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:55.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:55.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:55.014][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:55.016][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:55.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-18 12:59:55.019][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:55.020][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-18 12:59:55.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:55.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:55.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:55.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:55.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:55.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:55.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:55.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:55.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:55.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:55.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:55.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:55.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:55.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:55.041][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:55.043][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:55.044][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-18 12:59:55.044][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:55.045][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-18 12:59:55.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:55.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:55.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:55.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:55.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:55.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:55.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:55.052][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:55.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:55.055][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-18 12:59:55.055][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:55.056][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-18 12:59:55.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:55.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:55.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:55.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:55.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:55.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:55.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:55.063][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:55.065][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:55.066][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-18 12:59:55.066][rule$waitAsNeeded] Wait 0.299126 second(s).
biodb.TRACE[2025-03-18 12:59:55.371][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:55.480][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:55.568][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:55.569][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-18 12:59:55.571][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-18 12:59:55.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:55.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:55.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:55.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:55.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:55.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:55.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-18 12:59:55.582][biodb::testThat]
biodb.INFO [2025-03-18 12:59:55.582][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-18 12:59:55.583][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:55.583][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:55.585][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:55.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:55.588][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-18 12:59:55.588][rule$waitAsNeeded] Wait 0.00314784 second(s).
biodb.TRACE[2025-03-18 12:59:55.619][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:56.018][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:56.112][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:56.115][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-18 12:59:56.119][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-18 12:59:56.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:56.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.135][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:56.139][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:56.140][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:56.141][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:56.240][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:56.339][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:56.342][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-18 12:59:56.346][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-18 12:59:56.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:56.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-18 12:59:56.363][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-18 12:59:56.365][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-18 12:59:56.366][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-18 12:59:56.367][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-18 12:59:56.367][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.369][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.370][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-18 12:59:56.376][biodb::testContext]
biodb.INFO [2025-03-18 12:59:56.377][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:56.378][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-18 12:59:56.379][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:56.380][biodb::testContext]
biodb.INFO [2025-03-18 12:59:56.382][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:56.384][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:56.389][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:56.390][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-18 12:59:56.391][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-18 12:59:56.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.394][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-18 12:59:56.395][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-18 12:59:56.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.398][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-18 12:59:56.400][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-18 12:59:56.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.403][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-18 12:59:56.404][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-18 12:59:56.404][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-18 12:59:56.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.407][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-18 12:59:56.408][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-18 12:59:56.409][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-18 12:59:56.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.412][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-18 12:59:56.413][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-18 12:59:56.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.416][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-18 12:59:56.417][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-18 12:59:56.418][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-18 12:59:56.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.420][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-18 12:59:56.421][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-18 12:59:56.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.424][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-18 12:59:56.425][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-18 12:59:56.426][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-18 12:59:56.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.429][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:56.430][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-18 12:59:56.430][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-18 12:59:56.431][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-18 12:59:56.432][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-18 12:59:56.433][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-18 12:59:56.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.436][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-18 12:59:56.437][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-18 12:59:56.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.440][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-18 12:59:56.441][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-18 12:59:56.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.444][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-18 12:59:56.444][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-18 12:59:56.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.448][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-18 12:59:56.449][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-18 12:59:56.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.452][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-18 12:59:56.452][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-18 12:59:56.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.455][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:56.456][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-18 12:59:56.472][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-18 12:59:56.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.476][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-18 12:59:56.477][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-18 12:59:56.478][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-18 12:59:56.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.481][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-18 12:59:56.483][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.484][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-18 12:59:56.484][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.485][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:56.486][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.487][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.489][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:56.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:56.491][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.492][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-18 12:59:56.492][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:56.493][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.494][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:56.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:56.495][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:56.495][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:56.495][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:56.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:56.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.498][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:56.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.518][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:56.519][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:56.520][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.521][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.522][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-18 12:59:56.523][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.524][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:56.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:56.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.528][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.529][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.530][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:56.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:56.532][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.532][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-18 12:59:56.533][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:56.534][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.535][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.535][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:56.535][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:56.535][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:56.535][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:56.535][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:56.536][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:56.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.539][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:56.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.541][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.542][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.542][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:56.543][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:56.544][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.545][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.545][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-18 12:59:56.547][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.548][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-18 12:59:56.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:56.550][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.551][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.552][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.553][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.554][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:56.555][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:56.555][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.556][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-18 12:59:56.557][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:56.558][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.559][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.559][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.560][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:56.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.562][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:56.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.565][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.566][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.566][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:56.567][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:56.568][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.568][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.569][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-18 12:59:56.571][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.572][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:56.573][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.573][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:56.574][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.575][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.576][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.577][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.577][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:56.578][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:56.579][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.580][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-18 12:59:56.581][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:56.581][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.582][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.583][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.584][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:56.585][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.586][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:56.587][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.588][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.589][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.590][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:56.591][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:56.591][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.592][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:56.593][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:56.594][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.656][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-18 12:59:56.657][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-18 12:59:56.659][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-18 12:59:56.660][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-18 12:59:56.661][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:56.662][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:56.663][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:56.665][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:56.666][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-18 12:59:56.667][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:56.668][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:56.669][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-18 12:59:56.670][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:56.671][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:56.673][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-18 12:59:56.674][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:56.675][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-18 12:59:56.676][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-18 12:59:56.677][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:56.678][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-18 12:59:56.679][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-18 12:59:56.681][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-18 12:59:56.682][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-18 12:59:56.683][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-18 12:59:56.684][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-18 12:59:56.685][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-18 12:59:56.686][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-18 12:59:56.687][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-18 12:59:56.689][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-18 12:59:56.690][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-18 12:59:56.691][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-18 12:59:56.692][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-18 12:59:56.693][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-18 12:59:56.694][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-18 12:59:56.696][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-18 12:59:56.697][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-18 12:59:56.698][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-18 12:59:56.699][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-18 12:59:56.700][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-18 12:59:56.701][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-18 12:59:56.702][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-18 12:59:56.704][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-18 12:59:56.705][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-18 12:59:56.706][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-18 12:59:56.707][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-18 12:59:56.708][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-18 12:59:56.709][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-18 12:59:56.710][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-18 12:59:56.712][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-18 12:59:56.713][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-18 12:59:56.714][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-18 12:59:56.715][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-18 12:59:56.717][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-18 12:59:56.718][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-18 12:59:56.719][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-18 12:59:56.720][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-18 12:59:56.721][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-18 12:59:56.723][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-18 12:59:56.724][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-18 12:59:56.725][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-18 12:59:56.726][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-18 12:59:56.727][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-18 12:59:56.728][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-18 12:59:56.730][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-18 12:59:56.731][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-18 12:59:56.732][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-18 12:59:56.733][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:56.734][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:56.735][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-18 12:59:56.736][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-18 12:59:56.738][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-18 12:59:56.739][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-18 12:59:56.740][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-18 12:59:56.741][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-18 12:59:56.742][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-18 12:59:56.743][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-18 12:59:56.744][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-18 12:59:56.746][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-18 12:59:56.747][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-18 12:59:56.748][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-18 12:59:56.749][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-18 12:59:56.750][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-18 12:59:56.751][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-18 12:59:56.753][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-18 12:59:56.755][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:56.755][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:56.756][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.758][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:56.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:56.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:56.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:56.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:56.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:56.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:56.852][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:56.854][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-18 12:59:56.856][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.857][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.858][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.858][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:56.859][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.860][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.861][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.862][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-18 12:59:56.863][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-18 12:59:56.863][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:56.864][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.865][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-18 12:59:56.866][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-18 12:59:56.867][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-18 12:59:56.868][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:56.869][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:56.869][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:56.869][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:56.870][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-18 12:59:56.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.872][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:56.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:56.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:56.875][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:56.876][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:56.876][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-18 12:59:56.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:56.877][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:56.878][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:56.879][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-18 12:59:56.879][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-18 12:59:56.880][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:56.881][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:56.883][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-18 12:59:56.884][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:56.886][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:56.887][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:56.890][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-18 12:59:56.891][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-18 12:59:56.892][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-18 12:59:56.894][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-18 12:59:56.895][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:56.896][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:56.898][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-18 12:59:56.899][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-18 12:59:56.900][biodb::testThat]
biodb.INFO [2025-03-18 12:59:56.901][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-18 12:59:56.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:56.903][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:56.906][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-18 12:59:56.910][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:56.911][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-18 12:59:56.912][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:56.914][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-18 12:59:56.917][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:56.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:56.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:56.924][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-18 12:59:57.012][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-18 12:59:57.101][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-18 12:59:57.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-18 12:59:57.108][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-18 12:59:57.118][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-18 12:59:57.119][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-18 12:59:57.120][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-18 12:59:57.121][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-18 12:59:57.122][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.123][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.125][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-18 12:59:57.130][biodb::testContext]
biodb.INFO [2025-03-18 12:59:57.131][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:57.132][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-18 12:59:57.133][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:57.134][biodb::testContext]
biodb.INFO [2025-03-18 12:59:57.136][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:57.138][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:57.143][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:57.144][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-18 12:59:57.145][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-18 12:59:57.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.148][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-18 12:59:57.149][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-18 12:59:57.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.152][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-18 12:59:57.152][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-18 12:59:57.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.155][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-18 12:59:57.156][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-18 12:59:57.157][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-18 12:59:57.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.160][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-18 12:59:57.160][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-18 12:59:57.161][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-18 12:59:57.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.164][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-18 12:59:57.165][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-18 12:59:57.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.168][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-18 12:59:57.169][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-18 12:59:57.169][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-18 12:59:57.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.172][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-18 12:59:57.173][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-18 12:59:57.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.176][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-18 12:59:57.177][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-18 12:59:57.178][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-18 12:59:57.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.181][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:57.182][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-18 12:59:57.182][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-18 12:59:57.183][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-18 12:59:57.184][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-18 12:59:57.185][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-18 12:59:57.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.188][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-18 12:59:57.189][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-18 12:59:57.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.192][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-18 12:59:57.193][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-18 12:59:57.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.196][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-18 12:59:57.197][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-18 12:59:57.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.199][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-18 12:59:57.200][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-18 12:59:57.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.203][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-18 12:59:57.204][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-18 12:59:57.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.207][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:57.208][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-18 12:59:57.225][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-18 12:59:57.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.229][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-18 12:59:57.230][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-18 12:59:57.231][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-18 12:59:57.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.234][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-18 12:59:57.236][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.237][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-18 12:59:57.238][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.239][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:57.239][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.241][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.242][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.243][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:57.243][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:57.244][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.245][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-18 12:59:57.246][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:57.247][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.248][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.248][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:57.248][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:57.248][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:57.248][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:57.248][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:57.249][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:57.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.252][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:57.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.255][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:57.256][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:57.257][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.258][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.259][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-18 12:59:57.261][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.261][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:57.262][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.263][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:57.264][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.265][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.265][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.267][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:57.268][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:57.269][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.269][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-18 12:59:57.270][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:57.271][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.272][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.273][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:57.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:57.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:57.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:57.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:57.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:57.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.277][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:57.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.286][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.291][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.291][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:57.292][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:57.293][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.294][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.295][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-18 12:59:57.296][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.297][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-18 12:59:57.298][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.299][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:57.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.302][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.303][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.304][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.304][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:57.307][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:57.308][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.309][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-18 12:59:57.310][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:57.310][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.311][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.312][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.313][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:57.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.315][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:57.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.318][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.318][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.319][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:57.320][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:57.321][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.321][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.322][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-18 12:59:57.324][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.325][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:57.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.327][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:57.328][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.328][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.329][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.330][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.331][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:57.332][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:57.332][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.333][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-18 12:59:57.334][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:57.335][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.336][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.336][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:57.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:57.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.342][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.343][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.343][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:57.344][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:57.345][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.346][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:57.347][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:57.347][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.411][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-18 12:59:57.412][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-18 12:59:57.414][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-18 12:59:57.415][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-18 12:59:57.416][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:57.418][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:57.419][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:57.420][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:57.421][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-18 12:59:57.422][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:57.423][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:57.425][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-18 12:59:57.426][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:57.427][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:57.428][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-18 12:59:57.429][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:57.430][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-18 12:59:57.432][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-18 12:59:57.433][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:57.434][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-18 12:59:57.435][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-18 12:59:57.436][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-18 12:59:57.437][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-18 12:59:57.438][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-18 12:59:57.440][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-18 12:59:57.441][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-18 12:59:57.442][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-18 12:59:57.443][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-18 12:59:57.444][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-18 12:59:57.445][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-18 12:59:57.447][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-18 12:59:57.448][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-18 12:59:57.449][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-18 12:59:57.450][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-18 12:59:57.451][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-18 12:59:57.452][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-18 12:59:57.453][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-18 12:59:57.455][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-18 12:59:57.456][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-18 12:59:57.457][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-18 12:59:57.458][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-18 12:59:57.459][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-18 12:59:57.461][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-18 12:59:57.462][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-18 12:59:57.463][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-18 12:59:57.464][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-18 12:59:57.465][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-18 12:59:57.467][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-18 12:59:57.468][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-18 12:59:57.469][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-18 12:59:57.470][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-18 12:59:57.471][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-18 12:59:57.472][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-18 12:59:57.474][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-18 12:59:57.475][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-18 12:59:57.476][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-18 12:59:57.477][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-18 12:59:57.478][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-18 12:59:57.479][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-18 12:59:57.481][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-18 12:59:57.482][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-18 12:59:57.483][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-18 12:59:57.485][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-18 12:59:57.486][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-18 12:59:57.488][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-18 12:59:57.489][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-18 12:59:57.490][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:57.491][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:57.493][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-18 12:59:57.494][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-18 12:59:57.495][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-18 12:59:57.496][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-18 12:59:57.497][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-18 12:59:57.499][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-18 12:59:57.500][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-18 12:59:57.501][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-18 12:59:57.502][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-18 12:59:57.503][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-18 12:59:57.505][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-18 12:59:57.506][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-18 12:59:57.507][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-18 12:59:57.509][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-18 12:59:57.510][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-18 12:59:57.511][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-18 12:59:57.513][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:57.514][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:57.515][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.516][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:57.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.611][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:57.613][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-18 12:59:57.615][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.616][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.617][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.618][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:57.618][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.619][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.620][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.621][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-18 12:59:57.622][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-18 12:59:57.622][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:57.623][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.624][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-18 12:59:57.625][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-18 12:59:57.626][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-18 12:59:57.627][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:57.628][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:57.628][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:57.628][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:57.628][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-18 12:59:57.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.631][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:57.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:57.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:57.633][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:57.634][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:57.634][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-18 12:59:57.634][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:57.635][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:57.636][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:57.637][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-18 12:59:57.637][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-18 12:59:57.638][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:57.639][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:57.641][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-18 12:59:57.642][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:57.644][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:57.645][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:57.648][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-18 12:59:57.649][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-18 12:59:57.651][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-18 12:59:57.652][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-18 12:59:57.653][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:57.654][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:57.656][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-18 12:59:57.657][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-18 12:59:57.659][biodb::testThat]
biodb.INFO [2025-03-18 12:59:57.659][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-18 12:59:57.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:57.661][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:57.664][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-18 12:59:57.668][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:57.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-18 12:59:57.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:57.672][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-18 12:59:57.676][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-18 12:59:57.680][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-18 12:59:57.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-18 12:59:57.682][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:57.684][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-18 12:59:57.688][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-18 12:59:57.689][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-18 12:59:57.691][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-18 12:59:57.692][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:57.693][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:57.694][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:57.695][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-18 12:59:57.696][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-18 12:59:57.696][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-18 12:59:57.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:57.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:57.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:57.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:57.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:57.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:57.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:57.710][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-18 12:59:57.713][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-18 12:59:57.714][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-18 12:59:57.715][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-18 13:00:03.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-18 13:00:03.757][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-18 13:00:03.759][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-18 13:00:03.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-18 13:00:03.766][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-18 13:00:03.768][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-18 13:00:03.769][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-18 13:00:03.770][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-18 13:00:03.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 13:00:03.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 13:00:03.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 13:00:03.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 13:00:03.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 13:00:03.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 13:00:03.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 13:00:03.786][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.790][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.795][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 13:00:03.796][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 13:00:03.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.798][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.800][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-18 13:00:03.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-18 13:00:03.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.803][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 13:00:03.804][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 13:00:03.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 13:00:03.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 13:00:03.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.810][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 13:00:03.811][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 13:00:03.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.814][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 13:00:03.816][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 13:00:03.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.818][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 13:00:03.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 13:00:03.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.821][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.822][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 13:00:03.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 13:00:03.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.826][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 13:00:03.827][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 13:00:03.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.829][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-18 13:00:03.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-18 13:00:03.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.833][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 13:00:03.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 13:00:03.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.835][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 13:00:03.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 13:00:03.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.840][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 13:00:03.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 13:00:03.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 13:00:03.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 13:00:03.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.847][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 13:00:03.848][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 13:00:03.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.850][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.851][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-18 13:00:03.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-18 13:00:03.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.855][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 13:00:03.856][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 13:00:03.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.860][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 13:00:03.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 13:00:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 13:00:03.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 13:00:03.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 13:00:03.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 13:00:03.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 13:00:03.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 13:00:03.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 13:00:03.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 13:00:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 13:00:03.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 13:00:03.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 13:00:03.899][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-18 13:00:03.904][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-18 13:00:03.905][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-18 13:00:03.906][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-18 13:00:03.907][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-18 13:00:03.908][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 13:00:03.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 13:00:03.909][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 13:00:03.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 13:00:03.911][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 13:00:03.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
17.659 1.135 41.915
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.469 | 0.673 | 3.403 | |
| ChebiEntry | 0.421 | 0.018 | 0.440 | |